[Biococoa-dev] BCPairwiseAlignment & BCScoreMatrix
Koen van der Drift
kvddrift at earthlink.net
Fri Mar 11 18:18:35 EST 2005
On Mar 11, 2005, at 4:31 PM, Alexander Griekspoor wrote:
> So Koen, in this light your remark:
>> I am thinking how this will be used. The end user probably wants to
>> try out one type of alignment, see the result, then try another one,
>> compare the results, etc. So if we make a BCNeedlemanWunsch, and then
>> a BCSmithWaterman where is the actual matrix that is used to
>> calculate. I think it is a good idea if we have just one matrix, that
>> is used as a basis for each different calculation. It would be a
>> waste if for every calculation the starting matrix has to be
>> re-calculated. Or maybe that's where BCMatrix comes in place?
> The actual matrix used for calculation is the second one. But keeping
> the matrix only saves you the memory allocation, but different
> alignments fill the matrix differently so there's no use in keeping it
> around as it has to be refilled again with scores based on algorithm,
> penalty scores, gap costs etc. As most time goes into filling the
> matrix and tracing it back after the fill, you can't reuse it. Also,
> most algorithms that are subquadratic for memory requirements, chop up
> the matrix and use a divide-and-conquer approach because it's the
> storage of a complete-sized matrix that forms the memory problem.
> Does this make any sense?
>
Yes :)
- Koen.
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